What is Epigenetics technical articles are geared towards epigenetic research techniques, news, and trends in the field of epigenetics, written by scientists from universities and institutions including UCLA, Hofstra, NIH, Johns Hopkins, and more.

Explore in detail new epigenetic research techniques and tips for topics like next-generation sequencing (NGS) in epigenetics, m6A RNA methylation, CRISPR/Cas9 system epigenetic editing, chromatin immunoprecipitation (ChIP) protocol optimization, and single-cell epigenomics methods.

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Novel Assay to Probe the DNA Methylation State of Multiple Genomic Loci in Single Cells

October 1, 2013 WhatIsEpigenetics

The scientists from A*STAR’s Institute of Medical Biology (IMB) and Institute of Molecular and Cell Biology (IMCB)  developed a novel methodology to probe single cells for various DNA-methylation errors at multiple loci to reveal failed maintenance of epigenetic mark results in chimeric mice, which display unpredictable phenotypes leading to developmental arrest. This methodology allows the use of  a special technique utilizing a microfluidic device to safely extract one cell for performing the assay called “pronuclear transfer” to ameliorate reprogramming defects in embryos. This study not [more…]

Chromatin Remodelers Fine-Tune H3K36me-Directed Deacetylation of Neighbor Nucleosomes by Rpd3S

September 30, 2013 Milka Rodriguez

To form chromatin, DNA is tightly wrapped around nuclear proteins called histones. The repeating DNA-histone complex, which consists of 146 base pairs of double-stranded DNA wrapped around eight core histone proteins (H2A, H2B, H3 and H4), is called a nucleosome. Histone proteins are involved in structural organization of chromatin in eukaryotic cells. They can undergo various posttranslational modifications (PTMs) such as methylation/demethylation and acetylation/deacetylation, which can alter their interaction with DNA and nuclear proteins resulting in remodeling of chromatin structure [more…]

Epigenetic Memory at Embryonic Enhancers Identified in DNA Maps from Adult Mouse Tissues

September 13, 2013 Milka Rodriguez

In human DNA, 5-methylcytosine is found in approximately 1.5% of genomic DNA. In somatic cells, 5-mC occurs almost exclusively in the context of paired symmetrical methylation of a CpG site. An exception to this is seen in embryonic stem (ES) cells, where a substantial amount of 5-mC is also observed in non-CpG contexts. In the bulk of genomic DNA, most CpG sites are heavily methylated while CpG islands (sites of CpG clusters) in germ-line tissues and located near promoters of [more…]

Sequence-specific microscopic visualization of DNA methylation status at satellite repeats in individual cell nuclei and chromosomes

September 13, 2013 WhatIsEpigenetics

Scientists from Japan developed methylation-specific fluorescence in situ hybridization (MeFISH) for microscopic visualization of DNA methylation status at specific repeat sequences in individual cells. MeFISH is based on the differential reactivity of 5-methylcytosine and cytosine in target DNA for interstrand complex formation with osmium and bipyridine-containing nucleic acids (ICON). Cell nuclei and chromosomes hybridized with fluorescence-labeled ICON probes for mouse major and minor satellite repeats were treated with osmium for crosslinking. After denaturation, fluorescent signals were retained specifically at satellite [more…]

Illumina Doubles Output of Benchtop Sequencer MiSeq to 15 Gb

August 26, 2013 WhatIsEpigenetics

San Diego-based Illumina, Inc. doubles the sequencing output of its benchtop sequencer MiSeq to 15 gigabases (Gb) by increasing the number of sequencing reads to up to 25 million reads and overall read length to up to 2×300 base pairs. Subsequently, researchers can perform additional new applications on the MiSeq, including exome sequencing. Transcriptome applications such as mRNA sequencing can be supported now as well. Increased paired-end read lengths also improves the quality of genome assemblies, thereby advancing applications that [more…]

Identifying Site Specific Methylation in tRNAs and Target Substrates of RNA Methyltransferase NSun2

August 26, 2013 Milka Rodriguez

Currently, DNA methylation is one of the most broadly studied and well-characterized epigenetic modifications associated with gene silencing. The biological importance of 5-mC as a major epigenetic modification in phenotype and gene expression has been widely recognized. DNA hypomethylation is likely caused by methyl-deficiency due to a variety of environmental influences and has been proposed as a molecular marker in multiple biological processes such as cancer. The quantification of 5-mC content or global methylation in diseased or environmentally impacted cells [more…]

System for Optical Control of Mammalian Endogenous Transcription and Epigenetic States

August 26, 2013 WhatIsEpigenetics

Robust and versatile technologies that enable optical modulation of transcription in the mammalian endogenous genome have been difficult to achieve for a while. To solve this problem, scientists at the Broad Institute of MIT and Harvard developed light-inducible transcriptional effectors (LITEs) — an optogenetic two-hybrid system integrating the TALE DNA-binding domain with a light-sensitive cryptochrome 2 protein and its partner CIB1 from the Arabidopsis thaliana plant. LITEs can be customized to target many endogenous genomic loci and can be quickly [more…]

In-Depth Analysis of 42 Whole-Genome Bisulfite Sequencing Data Carried Out by Broad Institute

August 24, 2013 WhatIsEpigenetics

Scientists from Broad Institute of MIT and Harvard report in-depth analysis of 42 whole-genome bisulfite sequencing data sets across 30 diverse human cell and tissue types. This study tries to answer when, where, and how many CpGs are involved in genomic regulation. Within a normal developmental context, the scientists observed dynamic regulation for only 21.8% of autosomal CpGs, most of which are situated away from transcription start sites. These dynamic CpGs co-localize with enhancers and transcription-factor-binding sites, allowing for identification [more…]

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